Changes

The bam executable has the following functions.

The bam executable has the following functions.

* [[BamUtil: validate|validate|validate - Read and Validate a SAM/BAM file]]

 

* [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]

 

* [[BamUtil: dumpHeader|dumpHeader - Print SAM/BAM header]]

* Rewrite SAM/BAM Files

* [[BamUtil: splitChromosome|splitChromosome - Split BAM by Chromosome]]

** [[BamUtil: convert|convert - Read a SAM/BAM file and write as a SAM/BAM file (optionally converts between '=' & bases in the sequence)]]

* [[BamUtil: writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region]]

** [[BamUtil: splitChromosome|splitChromosome - Split BAM by Chromosome]]

* [[BamUtil: dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]

** [[BamUtil: writeRegion|writeRegion - Write the alignments in the indexed BAM file that fall into the specified region and/or have the specified read name]]

* [[BamUtil: dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]

** [[BamUtil: filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]

* [[BamUtil: readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]

** [[BamUtil: revert|revert - Revert SAM/BAM replacing the specified fields with their previous values (if known) and removes specified tags]]

* [[BamUtil: filter|filter - Filter reads by clipping ends with too high of a mismatch percentage and by marking reads unmapped if the quality of mismatches is too high]]

** [[BamUtil: squeeze|squeeze - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores, and replacing readNames with unique integers]]

* [[BamUtil: readReference|readReference - Print the reference string for the specified region]]

** [[BamUtil: findCigars|findCigars - Output just the reads that contain any of the specified CIGAR operations]]

* [[BamUtil: diff|diff - Print the diffs between 2 bams]]

** [[BamUtil: readIndexedBam|readIndexedBam - Read an indexed BAM file reference by reference id -1 to the max reference id and write it out as a SAM/BAM file]]

* [[BamUtil: stats|stats - Print the diffs between 2 bams]]

 

* [[BamUtil: revert|revert - Revert SAM/BAM replacing the specified fields with their previous values (if known).]]

* [[BamUtil: squeeze|squeeze - reduces files size by dropping OQ fields, duplicates, specified tags, using '=' when a base matches the reference, binning quality scores.]]

** [[BamUtil: validate|validate|validate - Read and Validate a SAM/BAM file]]

* [[BamUtil: findCigars|findCigars - Output just the reads that contain any of the specified CIGAR operations.]]

** [[BamUtil: diff|diff - Print the diffs between 2 bams]]

** [[BamUtil: stats|stats - Print the diffs between 2 bams]]

 

** [[BamUtil: dumpHeader|dumpHeader - Print SAM/BAM header]]

** [[BamUtil: dumpRefInfo|dumpRefInfo - Print SAM/BAM Reference Information]]

** [[BamUtil: dumpIndex|dumpIndex - Dump a BAM index file into an easy to read text version]]

** [[BamUtil: readReference|readReference - Print the reference string for the specified region]]

 

This executable is built using [[C++ Library: libStatGen]].

This executable is built using [[C++ Library: libStatGen]].

Just running ./bam will print the Usage information for the bam executable.

Just running ./bam will print the Usage information for the bam executable.